I would consider reporting the SSA-1099 as received and then entering an item of negative Other Income (something like "Medicare premium refund inappropriately reported on SSA-1099") for the amount that the reporting of this as a Social Security benefit raised the amount on Form 1040 line 6b. That would allow the reporting on line 6b to agree with what the IRS will expect to be on line 6b and avoid a different amount there being flagged as a reporting error.
